Discover the fascinating world of genetic genealogy! Written for the non-scientist, YGG is the best source for unbiased news on the major genealogy DNA testing companies.
Written by CeCe Moore, an independent professional genetic genealogist and television consultant.

Saturday, February 9, 2013

A Visit to Family Tree DNA's State-of-the-Art Lab

I have been a bit behind in my postings, but I didn't want to miss the chance to write about the incredible lab tour of Family Tree DNA's awesome facility, which was definitely one of the highlights of the 2012 FTDNA Administrator's Conference for me. I don't know if you all realize it, but Family Tree DNA is the ONLY company in the field that has their very own lab. They process everything from start to finish in their state-of-the-art facility in Houston for the thousands of different DNA tests that they offer. (Thomas Krahn notes that the individual Y-SNP tests alone number over 2900!) Some people might find it comforting to know that when ordering a test through FTDNA, this very trustworthy company is the sole handler of their DNA sample.

Bennett Greenspan, CEO of FTDNA with stored B-Swab Samples

This lab is even capable of processing exome and whole genome sequences. (These are available through Family Tree DNA's sister division DNA DTC, both a part of Gene by Gene). Max Blankfeld proudly told me that almost immediately after the announcement, they were already receiving orders for both tests. This is really exciting if you think about it. The first company to offer genetic genealogy testing is, according to The Genomics Law Report, also the only company currently offering these advanced tests-of-the-future in a "truly direct-to-consumer manner". ("Gene By Gene probably does represent, however, the only commercial company currently offering a whole genome sequence in a truly direct-to-consumer (DTC) manner." DNA DTC: The Return of Direct to Consumer Whole Genome Sequencing, Dan Vorhaus, November 29, 2012)Okay, on to the lab tour! Tim Janzen has kindly shared both his notes and his photos with my readers. I have added to Tim's notes just a bit, but most of what you see below was written by him. (I lost my notes and, although I did use some of them,the photos from my cell phone aren't as nice as Tim's photos from a "real" camera!)

Tim was smiling like this pretty much the entire tour!

On November 12,
2012, Family Tree DNA graciously allowed approximately 30 attendees from
the FTDNA conference to take one-hour tours of their laboratory
facilities in Houston, Texas. Bennett Greenspan,
the president of FTDNA, primarily led the tours and Max Blankfeld led
some supplemental tours (for those of us who showed up late!). The
tour participants all donned lab jackets for the tour, making us feel very official (I got to be Thomas Krahn). Bennett
explained
the functions of a number of very important pieces of DNA equipment as
he took us through the lab. (Update - Thomas Krahn has added some very interesting and educational commentary throughout this post. I have added it below or just after what it is referencing. Thanks Thomas!)

"Your Genetic Genealogist" parading as Thomas Krahn
Do you think I fooled anyone?

One of the first pieces of equipment
we viewed is used to extract the DNA from samples that are sent to
FTDNA. The DNA is extracted through an automated
process.Ninety-six samples can be processed at
a time. FTDNA can complete 600 extractions per day and has a 98.8% success rate of extracting DNA on the first try.

Another piece of equipment held primers that are used to test
for specific short tandem repeat (STR) tests and single nucleotide
polymorphism (SNP) tests. (Note from Thomas Krahn:
We're taking the DNA from
the DNA tubes and transferring them to a reaction plate which contains the primers and the rest of the PCR assay. In a previous step the primers were distributed in the correct wells by automatically picking the correct primer pair so that the customer gets the segment sequenced where the marker is located that he's interested in.)This process is also entirely robotized so that multiple
tests can be run at a time. The lab must repeatedly change the plastic
covers on the pipettes to ensure that DNA from
two different samples is never mixed as part of the testing.(Note from Thomas: We
use the covers just as a
precaution. In case a droplet is released from the pipetting tips during
the movement of the robot we want to make sure that the primer assays
are not contaminated with human DNA. With lids the primer library is
safe. We would easily recognize such a contamination because of mixed
basecalls, however primers are expensive and we want to protect the
primer library from such a contamination. The chance that DNA samples
mix is pretty small because we reduce the speed of the robot drastically
while we have the tips over the DNA plate. In any case such a cross contamination could probably not be prevented with a lid method. The pipetting tip is
discarded after the DNA from one person is distributed into all the
assays that he ordered. Each DNA sample gets a brand new tip so that
cross-contamination through the tip itself can be excluded.)

FTDNA's automated equipment that is used to combine DNA with primers

Bennett Greenspan
proudly showed off the robotic DNA storage freezer that the company
purchased in autumn of 2011. It was designed and manufactured by the
engineering company Matrical Bioscience in Spokane, Washington. This
piece of equipment took many months to design and build. After it had
been built, it was disassembled and shipped to Houston. The
installation process in the FTDNA lab took approximately 6 weeks. This chamber stores multiple small trays that hold 96 DNA samples each. The samples are held in small vials about 3/4
inch in height and about 3/8 inch in diameter. The trays holding the
samples are about 4 inches by 7 inches in size. There are thousands of
trays stacked on top of each other in a -20 degrees
Celsius chamber approximately 5 feet by 8 feet in size. A robot inside
this chamber retrieves DNA samples from the approximately 175,000
samples that are stored there in a very strictly regimented and automated
fashion. (Note from Thomas: I have just made a query
and there are currently 173,012 DNA tubes in the store. However more than 50% of them have been added during the last year. 500,000 is the approximate number when the store is 100% full. We have rigorously sorted out empty and bad tubes from our repository in the past and we run regularcompression procedures so that the racks are not half empty.)
This robot is wired to a computer station
outside the room. At the computer terminal a lab technician can enter a
series of kit numbers for DNA samples for which additional testing has
been ordered. The technician can then leave the area to do other things
while the robot automatically retrieves
the samples that were chosen. Ninety-six samples can be retrieved at a time and the retrieval process
takes approximately 30 minutes. When the retrieval process has been completed the technician
then returns to the storage unit, picks up the tray of samples and
takes it to another piece of equipment for the additional testing that the customer has ordered, such as upgraded STR panels or individual SNP tests.

The interior of the MiniStore storage chamber. The robot is retrieving samples.

The functions of other pieces of equipment in the lab were also explained by Bennett. One
machine is used for mitochondrial DNA sequencing. There is also another
piece of equipment that is used to lyse
the cells in each of the DNA samples and prepare them for extraction of
the DNA. Additionally, Bennett showed us a room that contains thousands of DNA
samples that have not yet been processed. These samples are held in
long-term storage at room temperature for eventual
use by customers who wish to order additional testing.

Bennett also took us to a different room where the Geno 2.0 SNP chip
tests are being processed. Approximately
154,000
SNPs are tested on a single chip for the Geno 2.0 test. Considering this, the chips
are relatively small at approximately 1 inch by 4 inches in
size. The actual scanning area is only 5mm by 5mm per assay. (Note from Thomas: On one of those glass slides there are 12 samples processed simultaneously.) At the time we were there, thousands of chips were being processed.

Bennett holding one of the Geno 2.0 SNP chips

Bennett showed us the new sequencing machines
that were recently purchased so that the company can do large-scale
complete genome sequencing. The
two new Illumina HiSeq 2000 machines can sequence 10 times as much as the
Applied Biosystems DNA Analyzers are capable of using 454 sequencing and can sequence a complete genome in
three runs. These machines are approximately 2000 times as efficient as
using the primers used in Walk Through the Y testing and are 100 times as
efficient as the Applied Biosystems 454 sequencer.
(Note from Thomas: The HiSeq instruments are producing more sequences so that you get a higher coverage. If the machines are also more "efficient" for finding new mutations by the same scaling factor is still to be demonstrated. Simply scaling the average coverage of 400 KB from the WTY times 2000 would yield 800 MB, however the Y chromosome is only 50 MB long and only 20 MB can be effectively aligned to the reference sequence. To overcome this problem you'll want to enrich for target specific DNA and you'll want to barcode several samples so that they can be pooled together on one instrument run. This again reduces the "efficiency" by quite some
significant percentage.)
FTDNA has two new Illumina MiSeq DNA sequencers as well. The lab now has the capability to sequence six whole genomes in two weeks and 64 exomes at 80x coverage in one week.

Bennett discussing the two new Illumina HiSeq 2000 high output DNA sequencers

The FTDNA lab tour was an exciting experience. It was very interesting to see all of the technicians at work running
the various DNA tests that we as FTDNA customers have ordered. I was incredibly impressed by their vast array of state-of-the-art equipment. Hopefully, Bennett and the rest of his lab
staff will continue to allow these tours for attendees at future FTDNA
conferences. If you haven't seen it yet, it is well worth your time and I highly recommend it. The following may be overkill for some of you. If so, I will just say goodbye to you here. However, if you are like me and you just can't get enough or want to gain a better understanding of how this all works from the inside, here is a series of photos from the lab tour.

Comment from Thomas:
FTDNA's automated equipment
that is used to combine genomic DNAwithprimers to prepare a PCR assay.An in-house developed software controlls the pipetting steps so that the ordered assay is run with the correct DNA.

Comment from Thomas: (This is) where the individual DNA sample tubes are re-arranged to the position where they will be processed in the assay. We try to prevent thaw and freeze cycles wherever possible because they will degrade DNA. So instead of taking out a complete plate (where we may only need a single sample) and thaw it completely, we use this technology of re-arraying tubes in the frozen state so that only the processed samples will be thawed and all other samples will stay frozen. The DNA samples/plates are actually stored in the back compartment and on the left side. Those areas are not clearly visible in the image.

The interior of the MiniStore storage chamberholds over 500,000 DNA samples
(seen at the back side)

One of the thousands of plastic trays that FTDNA uses to hold DNA samples

Shaking incubation chamber used to lyse cells so that DNA can be extracted

Comment from Thomas: The recipe for the liquid
in the sample vials is optimized for long term storage under a large variety of storage conditions. Essentially the high saltconcentration will suck out all water from inside the cheek cells (by osmosis) so that the cells form compact clumps and conserve their ingredients. This makes the sample more resistant to mechanical shearing and the high salt concentration also inhibits growth ofmicro-organisms that could digest the cells. The downside of this is that we need to use harsh mechanical forces when we enzymatically want to open the cells to extract the DNA. Shaking a 2 ml sample tube in an upright position doesn't really move the liquid in the tube a lot. Therefore we turn the tubes horizontally and shake them along the tube axis where the liquid has a longer path to accelerate. This method has been proven to be very effective.

Comment from Thomas: Before we dispose the chips
to the glass recycling facility, we temporarily store them for a few weeks. During a 48-hour time frame they are still good and since they are barcoded we may have the chance in rare cases to re-scan a chip in case some bad read happened at the scanner.

Bennett holding a box of 100 unprocessed samples being held in long-term storage

FTDNA's storage room where 1000s of unprocessed samples are held...

...Can you see yours?

Water purification system

Comment from Thomas: In order to get ultrapure
water for molecular genetic assays (such as PCR) the tap water needs to pass through several steps:
1.) Pre-filter to remove particles such as sand and rust from pipes
2.) Membrane filters to get rid of small particulate material
3.) Ion exchangers to remove Ions and salts
4.) Reverse osmosis to remove organic compounds. At this stage we use the water for general cleaning purpose such as for the lab dishwasher and for rinsing flasks. However to get PCR grade water we continue with:
5.) Another step of ion exchange and reverse osmosis in a laboratory grade water purification system to remove any contamination coming from the plastic tube piping internal of the lab.
6.) Then the water passes a sterile filter before it is bottled in a glass flask to remove bacteria and other micro-organisms.
7.) Finally the bottled water is heat sterilized in an autoclave at a temperature that should degrade all possible DNA chains that may have survived to this point.

We also have a room with two air compressors that supply compressed air for the robots. One of them is a backup system because at an interruption all robots will stand still. They are in a separate room across the hallway because they're quite noisy and produce a lot of heat.

Bennett with Geno 2.0 SNP chips

Illumina MiSeq machine

Bennett demo-ing the Illumina MiSeq machine

Automated pipetting system

Allied BioSystems 3730xl DNA Analyzer, used for sequencing

Comment from Thomas: Each lane represents a
sequencing trace where the bases are displayed in 4 different colors. This display format gives the technician a quick overview about the quality of the complete run. The fluorescence intensities are digitized by a analog to digital converter so that it can be saved on a computer, but they still represent analog measurement values. When talking about a digital output the impression could arise that the display shows the scored base-calls which is really processed in a later step.

Max Blankfeld leading the late arrivals

Bennett amuses Lauren (and the rest of us as well)

Did someone ask a question that stumped Bennett? Nah!

Ever wonder where your customer service calls go?

Jeremy happily assists customers

FTDNA employees preparing DNA test kits

Bye-bye FTDNA! See ya next year.

Thanks to Tim and Rachel Janzen for sharing their photos, Tim for helping to write this and to FTDNA for the spectacular tour.

That was so much fun! We even made it back in one piece! I also have many photos and I am just as guilty for not doing the write-up! One of these days. Hopefully I'll be more timely about sending you some shots from London in a couple of weeks. Thanks for posting about our adventure, CeCe!

Thanks for sharing all this Cece! Thanks to Tim and Rachel. So fascinating to see the goings on inside FTDNA. I don't know if I'll ever have the chance to tour, but would be in complete awe of it all if I did.Glad to see the technicians and other employees at work... I don't know if they ever get recognition. Thanks guys!!!So, next I will order the Geno 2.0 test. I hope the results are in by June, in time for the 1 day conference. As always, we appreciate your ongoing work CeCe and sharing great stuff on your blog!!

Hi Cece. I have been made aware of all your amazing work since ordering a test from AncestryDNA a few weeks ago. Your Ancestry.com profile and family tree popped up on my distant cousin match (5th-8th generation cousins) results. Your work is extraordinary! I've only scratched the surface of all your work and it is very exciting. I'm learning a great deal. Thank you for all you have done and for publicly sharing so much of your work. Best regards,Scott.

Instead of providing virtual tours, it would be nice if you processed the DNA sent your way. I submitted a sample back in Dec 2012, and have gotten nothing other than an acknowledgement (a couple of weeks ago) that you received it. Call me unimpressed ...

Thanks for sharing your photos CeCe. Just a little tidbit about myself....This is my day job - programming these robots. Well not ftDNA's robots. But these same robots that we have in MY lab. I guess I could program ftDNA's robots, if they wanted me to :-)